Reptiles demonstrate a vast geographical distribution, representing an important part of the world fauna, with more than 10.000 extant species (excluding their inner avian group). However, human activities, including climate change, degradation of natural habitats, urbanization and hunting, led to a dramatic decrease of natural populations the last decades and many species to the edge of extinction. Fortunately, numerous conservation projects are currently developed to protect threatened species. The identification of the sex, especially in species with slightly developed external sexual characters, is one of the biggest challenges for their successful conservation management. Recently, a large number of molecular methods have been developed for the fast, inexpensive and accurate sex identification. This study will summarize the current knowledge on molecular sexing of reptiles, offering valuable information for conservation management projects.